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Genome Evolution of The African Coelacanth and Tetrapod Evolution
Overview The coelacanth, which was previously thought to have gone extinct 70 million years ago, represents one of the genomes of the order of fish containing lobe-finned fish species - providing a link between modern ray-finned/cartilaginous fish and tetrapods. Coelacanths belong to the subclass Actinistia and are thus more closely related to lungfish, reptiles, and mammals than ray-finned fish.Additionally, they are related to numerous extinct Devonian fish species such as osteolepiforms, porolepiforms, rhizodonts, and Panderichthys. Originally, it was thought that this species of fish had gone extinct during the Cretaceous period. This remained true up until 1938, when a live coelacanth was caught in a fisherman's net off the coast of South Africa near the Chalumna River. This species appears to have changed very little since the Cretaceous period; with the species retaining their fleshy three-lobed caudal fins, round paddle-like tail (split into primary and secondary portions), cosmoid scales, bones, and joints. An interesting feature of this fish lies in it's intracranial joint found at the back of it's skull, which acts as a hinge to allow the fish to open its mouth wide. Unlike other fish, the coelacanth also retains its oil-filled notochord, which is present in early embryonic development and is typically replaced by a vertebral column. Additionally, the coelacanth has an abnormal heart and braincase - the heart's chambers are all arranged in a straight tube, while the braincase is primarily filled with fat (98.5%; only 1.5% contains brain tissue). Instead of having a swim bladder like most fish, the coelacanth has a fatty lung (a single-lobed vestigial lung) which it uses for buoyancy.The coelacanth also has an organ unique to its species: the rostral organ, which lies within the ethmoid region of the braincase near the snout and is filled with a gel-like substance, suggesting its function as an electroreceptive organ, enabling the organism to find prey in the dark. Purpose of the study This study looked to sequence the African coelacanth (Latimeria chalumnae) genome in order to analyze it's phylogenic relationship with its related species and gain insights into its genomic evolution. Genome Assembly and Annotation DNA samples from an African coelacanth found in the Comoros Islands was sequenced using an Ilumina platform and assembled using the short read genome assembler ALLPATHS-LG. "The draft assembly used is 2.86 gigabases in size and composed of 2.18 Gb plus gaps between contigs." According to the study, the coelacanth genome assembly has a contig of N50 size of 12.7 kilobases and a scaffold N50 size of 924 kb. The genome assembly was annotated separately by both the Ensemble and the MAKER. Ensemble: This gene annotation pipeline created gene models using protein alignments from limited amounts of complemenatry coelacanth DNA data and RNA-seq data generated from L. chalumnae muscle and orthology with other vertebrates from the Universal Protein Resource database - producing 19,033 protein-coding genes containing 21,817 transcripts. MAKER: This pipeline used the L. chalumnae Ensembl gene set, Uniprot protein alignments, samples from coelacanth muscle, liver, and testis, and RNA-seq data to create their gene models - producing 29,237 protein-coding gene annotations and 2,894 short non-coding RNAs, 1,214 long non-coding RNAs, and identifying more than 24,000 conserved RNA secondary structures. Results and Conclusions Based on the genome assembly and annotation, it was found that lungfish were more closely related to tetrapods than coelacanths. Scientists also found a region of the coelacanth HOX-A cluster that may have been involved in the evolution of extra-embryonic structures in tetrapods. "Global alignment of the coelacanth Hoxa14–Hoxa13 region with the homologous regions of the horn shark, chicken, human and mouse revealed a CNE just upstream of the coelacanth Hoxa14 gene (Supplementary Fig. 17a). This conserved stretch is not found in teleost fishes but is highly conserved among horn shark, chicken, human and mouse despite the fact that the chicken, human and mouse have no Hoxa14orthologues, and that the horn shark Hoxa14 gene has become a pseudogene. This CNE, HA14E1, corresponds to the proximal promoter-enhancer region of the Hoxa14gene in Latimeria. HA14E1 is more than 99% identical between mouse, human and all other sequenced mammals, and would therefore be considered to be an ultra-conserved element42. The high level of conservation suggests that this element, which already possessed promoter activity, may have been coopted for other functions despite the loss of the Hoxa14 gene in amniotes " Additionally, it was found that coelacanth lacks immunoglobulin-M, which is extremely unusual, as these antibodies have been found in all vertebrate species so far. Instead, two IgW immunoglobulin genes were found, which are only found in lungfish and cartilaginous fish and are believed to have originated in the ancestor of jawed vertebrates, but are lost in teleosts and tetrapods. Though morphological stasis may be characteristic of the coelacanth, this does not mean the genome of the coelacanth has been in stasis. This study confirmed that the protein-coding genes show a decreased substitution rate in L. chalumnae ''compared to other vertebrates. However, there is no evidence of low genome plasticity. Though examination of gene families show either unusually high or low levels of directional selection indicative of adaptation in the coelacanth. This information may indicate which selective pressures acted on the evolution of this organism's genome. References Woolston, Chris, and Nature Magazine. "'Coelacanth' Genome Unlocked."''Scientific American Global RSS. Scientific American, 17 Apr. 2013. Web. 16 Nov. 2014. . Amemiya, Chris T; et al. "The African Coelacanth Genome Provides Insights into Tetrapod Evolution." Nature.com. Nature Publishing Group, 18 Apr. 2013. Web. 16 Nov. 2014. . Amemiya, C. T.; et al. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, 18 Apr. 2013. Web. 16 Nov. 2014. . Wiki: Coelacanth